Biology subjects

Barnes, B.

Publications and source records attributed to Barnes, B..

7 recordsLinked to original sources

bioRxiv2025

Transcriptome remodeling and adaptive preservation of muscle protein content in hibernating black bears

Hibernation is an energy-saving adaptation associated with physical inactivity. In contrast to most mammals, hibernating bears demonstrate limited loss of muscle mass and protein content over the prolonged periods of immobility and fasting during winter. This suggests that bears have natural adaptive mechanisms preserving muscle mass and functionality. To identify transcriptional changes that underlie molecular mechanisms attenuating muscle loss, we conducted a large-scale gene expression profiling (14,199 genes) by transcriptome sequencing in quadriceps of adult black bears, comparing hibernating animals (n=5) and summer active animals (n=5). Gene set enrichment analysis showed significant positive correlation between hibernating phenotype and expression changes of genes involved in translation, ribosome and the mTORC1 mediated signaling. In contrast, coordinated transcriptional reduction was detected for genes involved in catabolism of branched chain amino acid (BCAA) suggesting preservation of BCAA. These findings imply maintenance of protein biosynthesis through the mTORC1 signaling positively activated by availability of BCAA in muscle during hibernation. Support for this conclusion comes from overexpression of RRAGD and RRAGB, crucial regulator of the mTORC1 response to leucine availability, and up regulation of EIF4B, downstream target of the mTORC1 signaling. Consistent with the mTORC1 suppression of autophagy-dependent protein degradation, MAP1LC3A and ULK1 were down regulated in hibernating muscle. The maintenance of protein biosynthesis and decrease in protein catabolism through the mTORC1 signaling as response to BCAA availability likely contribute to the preservation of muscle protein through prolonged periods of immobility and fasting during hibernation.

genomics↗

bioRxiv2024

MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies

Epigenome-wide association studies (EWAS) are transforming our understanding of the interplay between epigenetics and complex human traits and phenotypes. We introduce the Methylation Screening Array (MSA), a new iteration of the Infinium technology for scalable and quantitative screening of trait associations of nuanced ternary-code cytosine modifications in larger, more inclusive, and stratified human populations. MSA integrates EWAS, single-cell, and cell-type-resolved methylome profiles, covering diverse human traits and diseases. Our first MSA applications yield multiple biological insights: we revealed a previously unappreciated role of 5-hydroxymethylcytosine (5hmC) in trait associations and epigenetic clocks. We demonstrated that 5hmCs complement 5-methylcytosines (5mCs) in defining tissues and cells epigenetic identities. In-depth analyses highlighted the cell type context of EWAS and GWAS hits. Using this platform, we conducted a comprehensive human 5hmC aging EWAS, discovering tissue-invariant and tissue-specific aging dynamics, including distinct tissue-specific rates of mitotic hyper- and hypomethylation rates. These findings chart a landscape of the complex interplay of the two forms of cytosine modifications in diverse human tissues and their roles in health and disease.

genomics↗

bioRxiv2022

DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse

We have developed a mouse Infinium DNA methylation array that contains 297,415 probes to capture the diversity of mouse DNA methylation biology. We present a mouse DNA methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, age, sex, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. ApcMin/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This MM285 mouse array is widely accessible to the research community, and will accelerate future high sample-throughput studies in this important model organism.

genomics↗

bioRxiv2021

A mammalian methylation array for profiling methylation levels at conserved sequences

Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures 36k CpGs that are well conserved across mammalian species. We designed a set of probes on the array that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others.

bioinformatics↗

bioRxiv2020

Classification of ovarian cancer cell lines using transcriptional profiles defines the five major pathological subtypes

Epithelial ovarian cancer (EOC) is a heterogenous disease consisting of five major pathologically distinct subtypes: High-grade serous ovarian carcinoma (HGSOC), low-grade serous (LGS), endometrioid, clear cell and mucinous carcinoma. Although HGSOC is the most prevalent subtype, representing approximately 75% of cases, a 2013 landmark study from Domcke et al., found that many frequently used ovarian cancer cell lines were not genetically representative of HGSOC tissue samples from The Cancer Genome Atlas. Although this work subsequently identified several rarely used cell lines to be highly suitable as HGSOC models, cell line selection for ovarian cancer research does not appear to have altered substantially in recent years. Here, we find that application of non-negative matrix factorisation (NMF) to the transcriptional profiles of 45 commonly used ovarian cancer cell lines exquisitely clusters them into five distinct classes, representative of the five main subtypes of EOC. This methodology was in strong agreement with Domcke et al., in identification of cell lines most representative of HGSOC. Furthermore, this robust classification of cell lines, including some previously not annotated or miss-annotated in the literature, now informs selection of the most appropriate models for all five pathological subtypes of ovarian cancer. Furthermore, using machine learning algorithms trained using the classification of the current cell lines, we are able provide a methodology for future classification of novel EOC cell lines.

cancer biology↗

bioRxiv2020

PARG inhibition induces replication catastrophe in ovarian cancer cells with down-regulated DNA replication genes

The discovery that PARP1/2 inhibitors selectively kill BRCA mutant cells has led to a paradigm shift in the treatment of women with homologous recombination (HR)-deficient high-grade serous ovarian cancer (HGSOC), driving unprecedented improvements in progression-free and, more recently, overall survival. However, because most HGSOC cases are not HR-defective, and are therefore unlikely to benefit from PARPi-based therapies, additional strategies will be required to improve outcomes for women with HR-proficient disease. To develop novel therapeutic strategies, considerable attention is now being focused on inhibitors targeting PARG, the poly(ADP ribose) glycohydrolase that counterbalances PARP1/2 activity. Here we characterise ten ovarian cancer cell lines in response to the PARG inhibitor PDD00017273, hereafter PARGi. We demonstrate that six lines are resistant while four are sensitive, and that sensitivity correlates with several markers of persistent DNA replication stress, DNA damage and replication catastrophe, namely the accumulation of asymmetric DNA replication fibres, {gamma}H2AX and RPA foci, KAP1 and Chk1 phosphorylation, a pre-mitotic cell cycle block and, following prolonged exposure, a pan-nuclear {gamma}H2AX phenotype that indicates RPA exhaustion. We demonstrate that PARGi-sensitive cell lines have down-regulated DNA replication genes, including components of the fork protection complex, namely TIMELESS, TIPIN and CLASPIN. These observations suggest that a subset of HGSOC may respond to PARG inhibitors and that "replication stress" gene expression signature could serve as a predictive biomarker to guide the design of clinical trials.

cancer biology↗

bioRxiv2017

Designing Anti-Zika Virus Peptides Derived from Predicted Human-Zika Virus Protein-Protein Interactions

The production of anti-Zika virus (ZIKV) therapeutics has become increasingly important as the propagation of the devastating virus continues largely unchecked. Notably, a causal relationship between ZIKV infection and neurodevelopmental abnormalities has been widely reported, yet a specific mechanism underlying impaired neurological development has not been identified. Here, we report on the design of several synthetic competitive inhibitory peptides against key pathogenic ZIKV proteins through the prediction of protein-protein interactions (PPIs). Often, PPIs between host and viral proteins are crucial for infection and pathogenesis, making them attractive targets for therapeutics. Using two complementary sequence-based PPI prediction tools, we first produced a comprehensive map of predicted human-ZIKV PPIs (involving 209 human protein candidates). We then designed several peptides intended to disrupt the corresponding host-pathogen interactions thereby acting as anti-ZIKV therapeutics. The data generated in this study constitute a foundational resource to aid in the multi-disciplinary effort to combat ZIKV infection, including the design of additional synthetic proteins.

synthetic biology↗